diff --git a/README.md b/README.md index cdfaa547..48b34b8d 100644 --- a/README.md +++ b/README.md @@ -13,10 +13,10 @@ New documentation for the new data loaders and module structure is under develop 3. [Module Features](#features) 4. [Loading Biosamples](#loading-biosamples) 5. [Loading Expression Data](#loading-expression-data) -6. [Protocols](#protocols) -7. [Viewing Data](#viewing-and-downloading-data) -9. [Administrative Pages](#administrative-pages) -10. [Example Files](#example-files) +6. [Viewing Data](#viewing-and-downloading-data) +7. [Administrative Pages](#administrative-pages) +8. [Protocols](#protocols) +9. [Example Files](#example-files) # Introduction Tripal Analysis: Expression is a [Drupal](https://www.drupal.org/) module built to extend the functionality of the [Tripal](http://tripal.info/) toolset. @@ -180,42 +180,14 @@ The biosample name will be taken as the name of the file minus the file extensio * **Regex for End of Data** - If the expression file has a footer, use this field to capture teh line that occurs after the end of expression data. This line of text and all text following will be ignored. #### Experimental Design Fields -The "Experimental Design" fields allow a complete description of the experimental design by implementing the [Chado MAGE design schema](http://gmod.org/wiki/Chado_Mage_Module). The Chado MAGE module uses the arraydesign, assay, quantification, and acquisition tables to describe an experiment. This is reflected in the following fields available to describe an experiment. +The "Experimental Design" fields allow a complete description of the experimental design by implementing the [Chado MAGE design schema](http://gmod.org/wiki/Chado_Mage_Module). The Chado MAGE module uses the arraydesign, assay, quantification, and acquisition tables to describe an experiment. The Tripal Analysis Expression creates generic instances of all these for you. -* **Biomaterial Provider** - The person or organization responsible for collecting the biosample. * **Array Design** - This is only applicable for microarray expression data. This may be left blank for experiments that do not utilize an array (ie next generation sequencing). - -#### Acquisition Details -This represents the quantification technique. In the case of a microarray, it is scanning, in the case of a sequencer, it is sequencing. The output of this process is a digitial image of an array for a microarray or a set of digital images or nucleotide base calls for a sequencer. - - * **Acquisition URI** - A web address to a page that describes the acquisition process. - * **Date Acquisition Run** - The date the acquisition was run. - * **Acquisition Protocol** - The acquisition protocol used in the experiment. (See protocol description below). - -#### Quantification Details - * **Units** - The units associated with the loaded values, such as FPKM. You may also update the units of your experiments using the **Quantification Units** admin page. - * **Date Quantification Run** - The date the quantification was run. - * **Quantification URI** - A web address to a page that describes the quantification process. - * **Quantification Operator** - The person or organization that ran the quantification. - * **Quantification Protocol** - The quantification protocol used in the experiment. (See protocol description below). - -![Experimental Design Fields](https://cloud.githubusercontent.com/assets/14822959/12991557/a4b0228e-d0dd-11e5-93de-2f206be6d5fe.png) -![Data Loader Fields](https://cloud.githubusercontent.com/assets/14822959/12991553/a4ade58c-d0dd-11e5-97d2-1096d78bb189.png) - - -# Protocols - -Acquisition, Quantification, Array Design, and Assays all utilize protocols to describe them. Think of protocols as the **experimental design**, and Acquisitions, Quantifications, Array Designs, and Assays as the experiment following that experimental design. -**Protocol Descripton** - The protocol content types can be created by navigating to **Add Tripal Content->Protocol**. A protocol can be used to add extra detail to an experimental design. A protocol can be used to describe the assay, acquisition, and quantification steps of the experiment design. A protocol can also be used to further describe the array design content type. The fields of a protocol are: -* **Protocol Name (must be unique - required)** -* **Protocol Link (Required)** - A web address to a page that describes the protocol. -* **Protocol Description** - A description of the protocol. -* **Hardware Description** - A description of the wardware used in the protocol. -* **Software Description** - A description of the software used in the protocol. -* **Protocol Type (required)** - The protocol type can acquisition, array design, assay, or quantification. The user can also create new protocol types by inserting new CVterms into the protocol type CV. -* **Publication** - A publication that describes the protocol. +>![file information portion of expression loader](example_files/doc_images/expression_loader_file_info.png) +>![experimental design portion of expression loader](example_files/doc_images/expression_loader_experimental_design.png) +> The expression loader accepts parameters describing your file, as well as some experimental design parameters. # Viewing and Downloading Data @@ -272,6 +244,24 @@ You can also assign quantification units to **all unitless quantifications** usi + +# Protocols + +Acquisition, Quantification, Array Design, and Assays all utilize protocols to describe them. Think of protocols as the **experimental design**, and Acquisitions, Quantifications, Array Designs, and Assays as the experiment following that experimental design. + +There is currently no support for inputting, or displaying, acquisitions, quantifications, or assays. The Expression module creates generic instances of these entities. + +**Protocol Descripton** - The protocol content types can be created by navigating to **Add Tripal Content->Protocol**. A protocol can be used to add extra detail to an experimental design. A protocol can be used to describe the assay, acquisition, and quantification steps of the experiment design. A protocol can also be used to further describe the array design content type. The fields of a protocol are: +* **Protocol Name (must be unique - required)** +* **Protocol Link (Required)** - A web address to a page that describes the protocol. +* **Protocol Description** - A description of the protocol. +* **Hardware Description** - A description of the wardware used in the protocol. +* **Software Description** - A description of the software used in the protocol. +* **Protocol Type (required)** - The protocol type can acquisition, array design, assay, or quantification. The user can also create new protocol types by inserting new CVterms into the protocol type CV. +* **Publication** - A publication that describes the protocol. + + + # Example Files ### Biomaterial Loader diff --git a/example_files/doc_images/expression_loader_experimental_design.png b/example_files/doc_images/expression_loader_experimental_design.png new file mode 100644 index 00000000..6748a2c9 Binary files /dev/null and b/example_files/doc_images/expression_loader_experimental_design.png differ diff --git a/example_files/doc_images/expression_loader_file_info.png b/example_files/doc_images/expression_loader_file_info.png new file mode 100644 index 00000000..486dbf97 Binary files /dev/null and b/example_files/doc_images/expression_loader_file_info.png differ