{%extends "phenotypes/add-phenotypes-base.html"%} {%from "flash_messages.html" import flash_all_messages%} {%from "macro-table-pagination.html" import table_pagination%} {%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} {%from "phenotypes/macro-display-preview-table.html" import display_preview_table%} {%from "phenotypes/macro-display-resumable-elements.html" import display_resumable_elements%} {%block title%}Phenotypes{%endblock%} {%block pagetitle%}Phenotypes{%endblock%} {%block lvl4_breadcrumbs%}
  • Add Phenotypes
    • {%endblock%} {%block frm_add_phenotypes_documentation%}

    This page will allow you to upload all the separate files that make up your phenotypes. Here, you will have to upload each separate file individually. If you want instead to upload all your files as a single ZIP file, click here.

    {%endblock%} {%block frm_add_phenotypes_elements%}
    File(s) Metadata
    Provide the character that separates the fields in your file(s). It should be the same character for all files (if more than one is provided).
    A tab character will be assumed if you leave this field blank. See documentation for more information.
    This specifies that lines that begin with the character provided will be considered comment lines and ignored in their entirety. See documentation for more information.
    This specifies strings in your file indicate that there is no value for a particular cell (a cell is where a column and row intersect). Provide a space-separated list of strings if you have more than one way of indicating no values. See documentation for more information.
    Data File(s)
    Provide a file that contains only the phenotype descriptions, the documentation for the expected format of the file.
    {{display_resumable_elements( "resumable-phenotype-descriptions", "phenotype descriptions", '

    Drag and drop the CSV file that contains the descriptions of your phenotypes here.

    The CSV file should be a matrix of phenotypes × descriptions i.e. The first column contains the phenotype names/identifiers whereas the first row is a list of metadata fields like, "description", "units", etc.

    If the format is transposed (i.e. descriptions × phenotypes) select the checkbox above.

    Please see the "Phenotypes Descriptions" documentation section below for more information on the expected format of the file provided here.

    ')}} {{display_preview_table( "tbl-preview-pheno-desc", "phenotype descriptions")}}
    Provide a file that contains only the phenotype data. See the documentation for the expected format of the file.
    {{display_resumable_elements( "resumable-phenotype-data", "phenotype data", '

    Drag and drop a CSV file that contains the phenotypes numerical data here. You can click the "Browse" button (below and to the right) to select the file from your computer.

    The CSV should be a matrix of samples × phenotypes, i.e. The first column contains the samples identifiers while the first row is the list of phenotypes identifiers occurring in the phenotypes descriptions file.

    If the format is transposed (i.e phenotypes × samples) select the checkbox above.

    Please see the "Phenotypes Data" documentation section below for more information on the expected format for the file provided here.

    ')}} {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}}
    {%if population.Family in families_with_se_and_n%}
    Provide a file that contains only the standard errors for the phenotypes, computed from the data above.
    {{display_resumable_elements( "resumable-phenotype-se", "standard errors", '

    Drag and drop a CSV file that contains the phenotypes standard-errors data here. You can click the "Browse" button (below and to the right) to select the file from your computer.

    The CSV should be a matrix of samples × phenotypes, i.e. The first column contains the samples identifiers while the first row is the list of phenotypes identifiers occurring in the phenotypes descriptions file.

    If the format is transposed (i.e phenotypes × samples) select the checkbox above.

    Please see the "Phenotypes Data" documentation section below for more information on the expected format of the file provided here.

    ')}} {{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
    Provide a file that contains only the number of samples/individuals used in the computation of the standard errors above.
    {{display_resumable_elements( "resumable-phenotype-n", "number of samples/individuals", '

    Drag and drop a CSV file that contains the samples\' phenotypes counts data here. You can click the "Browse" button (below and to the right) to select the file from your computer.

    The CSV should be a matrix of samples × phenotypes, i.e. The first column contains the samples identifiers while the first row is the list of phenotypes identifiers occurring in the phenotypes descriptions file.

    If the format is transposed (i.e phenotypes × samples) select the checkbox above.

    Please see the "Phenotypes Data" documentation section below for more information on the expected format of the file provided here.

    ')}} {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}}
    {%endif%} {%endblock%} {%block page_documentation%}

    Help

    Common Features

    The following are the common expectations for ALL the files provided in the form above:

    If you do not specify the separator character, then we will assume a TAB character was used as your separator.

    We also assume you might include comments lines in your files. In that case, if you do not specify what character denotes that a line in your files is a comment line, we will assume the # character.
    A comment MUST ALWAYS begin at the start of the line marked with the comment character specified.

    File Metadata

    We request some details about your files to help us parse and process the files correctly. The details we collect are:

    File separator
    The files you provide should be character-separated value (CSV) files. We need to know what character you used to separate the values in your file. Some common ones are the Tab character, the comma, etc.
    Providing that information makes it possible for the system to parse and process your files correctly.
    NOTE: All the files you upload MUST use the same separator.
    Comment character
    We support use of comment lines in your files. We only support one type of comment style, the line comment.
    This mean the comment begins at the start of the line, and the end of that line indicates the end of that comment. If you have a really long comment, then you need to break it across multiple lines, marking each line a comment line.
    The "comment character" is the character at the start of the line that indicates that the line is a line comment.
    No-Value indicator(s)
    Data in the real world is messy, and in some cases, entirely absent. You need to indicate, in your files, that a particular field did not have a value, and once you do that, you then need to let the system know how you mark such fields. Common ways of indicating "empty values" are, leaving the field blank, using a character such as '-', or using strings like "NA", "N/A", "NULL", etc.
    Providing this information will help with parsing and processing such no-value fields the correct way.

    file: Phenotypes Descriptions

    The data in this file is a matrix of phenotypes × metadata-fields. Please note we use the term "metadata-fields" above loosely, due to lack of a good word for this.

    The file MUST have columns in this order:

    Phenotype Identifiers
    These are the names/identifiers for your phenotypes. These names/identifiers are the same ones you will have in all the other files you are uploading.
    Descriptions
    Each phenotype will need a description. Good description are necessary to inform other people of what the data is about. Good description are hard to construct, so we provide advice on describing your phenotypes.
    Units
    Each phenotype will need units for the measurements taken. If there are none, then indicate the field is a no-value field.

    You can add more columns after those three if you want to, but these 3 MUST be present.

    The file would, for example, look like the following:

    id,description,units,…
    pheno10001|Central nervous system, behavior, cognition; …|mg|…
    pheno10002|Aging, metabolism, central nervous system: …|mg|…
    ⋮

    Note 01: The first usable row is the heading row.

    Note 02: This example demonstrates a subtle issue that could make your CSV file invalid — the choice of your field separator character.
    In the example above, we use the pipe character (|) as our field separator. This is because, if we follow the advice on how to write good descriptions, then we cannot use the comma as our separator – if we did, then our CSV file would be invalid because the system would have no way to tell the difference between the comma as a field separator, and the comma as a way to separate the "general category and ontology terms".

    file: Phenotype Data, Standard Errors and/or Sample Counts

    The data is a matrix of samples(or individuals) × phenotypes, e.g.

    # num-cases: 2549 # num-phenos: 13 id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…
    IND001,61.400002,49,62.5,55.099998,…
    IND002,54.099998,50.099998,53.299999,55.099998,…
    IND003,483,403,501,403,…
    IND004,49.799999,45.5,62.900002,NA,…
    ⋮

    where IND001,IND002,IND003,IND004,… are the samples/individuals/cases in your study, and pheno10001,pheno10002,pheno10004,pheno10004,… are the identifiers for your phenotypes.

    The lines beginning with the "#" symbol (i.e. # num-cases: 2549 and # num-phenos: 13 are comment lines and will be ignored

    In this example, the comma (,) is used as the file separator.

    {%endblock%} {%block sidebarcontents%} {{display_pheno_dataset_card(species, population, dataset)}} {%endblock%} {%block more_javascript%} {%endblock%}