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.
The following are the common expectations for ALL the
- files provided in the form above:
-
-
The file MUST be character-separated values (CSV)
- text file
-
The first row in the file MUST be a heading row, and
- will be composed of the list identifiers for all of
- samples/individuals/cases involved in your study.
-
The first column of data in the file MUST be the
- identifiers for all of the phenotypes you wish to upload.
-
-
-
-
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:
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.
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.
Select the zip file bundle containing information on the phenotypes you
- wish to upload, then click the "Upload Phenotypes" button below to
- upload the data.
-
If you wish to upload the files individually instead,
- click here.
-
See the File Formats section below
- to get an understanding of what is expected of the bundle files you
- upload.
Other files within the bundle will be ignored, for this feature.
-
The following section will detail the expectations for each of the
- different file types within the uploaded ZIP file bundle for phenotypes:
-
-
Control File
-
There MUST be one, and only one file that acts
- as the control file. This file can be:
-
-
a JSON file, or
-
a YAML file.
-
-
-
-
The control file is useful for defining things about the bundle such as:
-
-
The field separator value (default: sep: ','). There can
- only ever be one field separator and it MUST be the same
- one for ALL files in the bundle.
-
The comment character (default: comment.char: '#'). Any
- line that starts with this character will be considered a comment line and
- be ignored in its entirety.
-
Code for missing values (default: na.strings: 'NA'). You
- can specify more than one code to indicate missing values, e.g.
- {…, "na.strings": ["NA", "N/A", "-"], …}
-
-
-
pheno File(s)
-
These files are the main data files. You must have at least one of these
- files in your bundle for it to be valid for this step.
-
The data is a matrix of individuals × phenotypes by default, as
- below:
-
- id,10001,10002,10003,10004,…
- BXD1,61.400002,54.099998,483,49.799999,…
- BXD2,49,50.099998,403,45.5,…
- BXD5,62.5,53.299999,501,62.900002,…
- BXD6,53.099998,55.099998,403,NA,…
- ⋮
-
-
If the pheno_transposed value is set to True,
- then the data will be a phenotypes × individuals matrix as in the
- example below:
-
- id,BXD1,BXD2,BXD5,BXD6,…
- 10001,61.400002,49,62.5,53.099998,…
- 10002,54.099998,50.099998,53.299999,55.099998,…
- 10003,483,403,501,403,…
- 10004,49.799999,45.5,62.900002,NA,…
- ⋮
-
-
-
-
-
phenocovar File(s)
-
At least one phenotypes metadata file with the metadata values such as
- descriptions, PubMed Identifier, publication titles (if present), etc.
-
The data in this/these file(s) is a matrix of
- phenotypes × phenotypes-covariates. The first column is always the
- phenotype names/identifiers — same as in the R/qtl2 format.
-
phenocovar files should never be transposed!
-
This file MUST be present in the bundle, and have data for
- the bundle to be considered valid by our system for this step.
- In addition to that, the following are the fields that must be
- present, and
- have values, in the file before the file is considered valid:
-
-
description: A description for each phenotype. Useful
- for users to know what the phenotype is about.
-
units: The units of measurement for the phenotype,
- e.g. milligrams for brain weight, centimetres/millimetres for
- tail-length, etc.
-
-
-
The following optional fields can also be provided:
-
-
pubmedid: A PubMed Identifier for the publication where
- the phenotype is published. If this field is not provided, the system will
- assume your phenotype is not published.
-
-
-
These files will be marked up in the control file with the
- phenocovar key, as in the examples below:
-
These are extensions to the R/qtl2 standard, i.e. these types ofs file are
- not supported by the original R/qtl2 file format
-
We use these files to upload the standard errors (phenose) when
- the data file (pheno) is average data. In that case, the
- phenonum file(s) contains the number of individuals that were
- involved when computing the averages.
-
Both types of files are matrices of individuals × phenotypes by
- default. Like the related pheno files, if
- pheno_transposed: True, then the file will be a matrix of
- phenotypes × individuals.
- The data has NOT been added/saved yet. Review the details below
- and click "Continue" to save the data.
-
The “{{dataset.FullName}}” dataset from the
- “{{population.FullName}}” population of the
- species “{{species.SpeciesName}} ({{species.FullName}})”
- will be updated as follows:
-
-
- {%if publication%}
-
All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes
- are linked to the following publication:
-
A total of {{summary[ftype]["number-of-files"]}} files will be processed
- adding {%if ftype == "phenocovar"%}(possibly){%endif%}
- {{summary[ftype]["total-data-rows"]}} new
- {%if ftype == "phenocovar"%}
- phenotypes
- {%else%}
- {{summary[ftype]["description"]}} rows
- {%endif%}
- to the database.
-
- {%endif%}
- {%endfor%}
-
-
-
-
-{%else%}
-
-
Invalid Job
-
- Could not find a job with the ID: {{job_id}}.
-
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-
-
- If you are not redirected, please
- click here to continue
-
-